pytomography 3.3.0__tar.gz → 3.3.2__tar.gz

{pytomography-3.3.0 → pytomography-3.3.2}/PKG-INFO

@@ -1,10 +1,11 @@
-Metadata-Version: 2.3
+Metadata-Version: 2.4
 Name: pytomography
-Version: 3.3.0
+Version: 3.3.2
 Summary: Package to perform tomographic image reconstruction
 Project-URL: Homepage, https://github.com/qurit/PyTomography
 Project-URL: Bug Tracker, https://github.com/qurit/PyTomography/issues
 Author-email: Luke Polson <lukepolson@outlook.com>
+License-File: LICENSE
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3
@@ -44,9 +45,14 @@ Description-Content-Type: text/markdown
 ![Stars](https://img.shields.io/github/stars/qurit/PyTomography)
 ![Issues](https://img.shields.io/github/issues/qurit/PyTomography)
 
-## How to get started?
+# Getting Started
 We have prepared a very detailed documentation guide available at [readthedocs](https://pytomography.readthedocs.io/en/latest/). If you have any additional questions, please ask them on the [discourse website](https://pytomography.discourse.group/).
 
+# Research Paper
+If you use PyTomography in your own research, please cite the corresponding research paper:
+
+**Lucas A. Polson, Roberto Fedrigo, Chenguang Li, Maziar Sabouri, Obed Dzikunu, Shadab Ahamed, Nicolas Karakatsanis, Sara Kurkowska, Peyman Sheikhzadeh, Pedro Esquinas, Arman Rahmim, and Carlos Uribe.** *PyTomography: A python library for medical image reconstruction.* SoftwareX, Volume 29, 2025, Page 102020. https://www.sciencedirect.com/science/article/pii/S235271102400390X
+
 # License
 This work is licensed under an MIT license, as is found in the LICENSE file.
 

{pytomography-3.3.0 → pytomography-3.3.2}/README.md

@@ -7,9 +7,14 @@
 ![Stars](https://img.shields.io/github/stars/qurit/PyTomography)
 ![Issues](https://img.shields.io/github/issues/qurit/PyTomography)
 
-## How to get started?
+# Getting Started
 We have prepared a very detailed documentation guide available at [readthedocs](https://pytomography.readthedocs.io/en/latest/). If you have any additional questions, please ask them on the [discourse website](https://pytomography.discourse.group/).
 
+# Research Paper
+If you use PyTomography in your own research, please cite the corresponding research paper:
+
+**Lucas A. Polson, Roberto Fedrigo, Chenguang Li, Maziar Sabouri, Obed Dzikunu, Shadab Ahamed, Nicolas Karakatsanis, Sara Kurkowska, Peyman Sheikhzadeh, Pedro Esquinas, Arman Rahmim, and Carlos Uribe.** *PyTomography: A python library for medical image reconstruction.* SoftwareX, Volume 29, 2025, Page 102020. https://www.sciencedirect.com/science/article/pii/S235271102400390X
+
 # License
 This work is licensed under an MIT license, as is found in the LICENSE file.
 

{pytomography-3.3.0 → pytomography-3.3.2}/docs/source/index.rst

@@ -7,7 +7,7 @@ PyTomography
 ``PyTomography`` is a python library for tomographic reconstruction of medical imaging data. It provides a modularized framework for the construction and development of system matrices, likelihoods, and reconstruction algorithms.
 
 .. note::
-     If you use PyTomography in your research, please cite `the corresponding research paper <https://arxiv.org/abs/2309.01977>`_.
+     If you use PyTomography in your research, please cite `the corresponding research paper <https://www.sciencedirect.com/science/article/pii/S235271102400390X>`_.
 
 ++++++++++++++++
 Getting Started

{pytomography-3.3.0 → pytomography-3.3.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "pytomography"
-version = "3.3.0"
+version = "3.3.2"
 
 
 authors = [

{pytomography-3.3.0 → pytomography-3.3.2}/src/pytomography/data/ct_table.csv

@@ -341,6 +341,9 @@ Energy,CT Energy,Model Name,Lower Coeff,Lower Constant,Upper Coeff,Upper Constan
 208,130,symbia t16,0.00014376,0.1352,0.00008787,0.1352
 208,140,infinia,0.00014328,0.1352,0.00009303,0.1352
 208,140,optima ct540,0.00014541,0.1352,0.00009102,0.1352
+218,80,symbia t2,0.00013308,0.1332,0.000061528,0.1332
+218,110,symbia t2,0.00013308,0.1332,0.000078047,0.1332
+218,130,symbia t2,0.00013308,0.1332,0.000086981,0.1332
 245,80,symbia intevo 16,0.00013481,0.1277,0.00005667,0.1277
 245,80,symbia t6,0.00013481,0.1277,0.00005667,0.1277
 245,80,symbia intevo 2,0.00013481,0.1277,0.00005667,0.1277
@@ -419,3 +422,6 @@ Energy,CT Energy,Model Name,Lower Coeff,Lower Constant,Upper Coeff,Upper Constan
 364,130,symbia t2,0.00011703,0.1102,0.00006868,0.1102
 364,140,infinia,0.00011679,0.1102,0.00007274,0.1102
 364,140,optima ct540,0.00011852,0.1102,0.00007117,0.1102
+440,80,symbia t2,0.00010195,0.10206,0.00004447,0.10206
+440,110,symbia t2,0.00010195,0.10206,0.00005641,0.10206
+440,130,symbia t2,0.00010195,0.10206,0.00006287,0.10206

{pytomography-3.3.0 → pytomography-3.3.2}/src/pytomography/io/SPECT/dicom.py

@@ -79,14 +79,17 @@ def parse_projection_dataset(
             angles = np.concatenate(
                 [angles, start_angle - delta_angle * np.arange(n_angles)]
             )
-        try:
-            radial_positions_detector = ds.DetectorInformationSequence[
-                detector - 1
-            ].RadialPosition
-        except AttributeError:
-            radial_positions_detector = ds.RotationInformationSequence[
-                detector - 1
-            ].RadialPosition
+        if ds.Manufacturer=='Mediso':
+            radial_positions_detector = ds.RotationInformationSequence[detector - 1].RadialPosition
+        else:
+            try:
+                radial_positions_detector = ds.DetectorInformationSequence[
+                    detector - 1
+                ].RadialPosition
+            except AttributeError:
+                radial_positions_detector = ds.RotationInformationSequence[
+                    detector - 1
+                ].RadialPosition
         if not isinstance(radial_positions_detector, collections.abc.Sequence):
             radial_positions_detector = n_angles * [radial_positions_detector]
         radii = np.concatenate([radii, radial_positions_detector])
@@ -539,8 +542,11 @@ def _get_affine_spect_projections(filename: str) -> np.array:
     dz = float(ds.PixelSpacing[1])
     if Sy == 0:
         Sx -= (ds.Rows-1) / 2 * dx
-        Sy -= (ds.Rows-2) / 2 * dy
+        Sy -= (ds.Rows-1) / 2 * dy
         Sy -= ds.RotationInformationSequence[0].TableHeight
+    elif ds.Manufacturer=='Mediso':
+        Sy = -(ds.Rows-1) / 2 * dy
+        #Sy = Sx
     Sz -= (ds.Rows-1) * dz # location of bottom pixel
     # Difference between Siemens and GE
     # if ds.Manufacturer=='GE MEDICAL SYSTEMS':

{pytomography-3.3.0 → pytomography-3.3.2}/src/pytomography/io/shared/dicom.py

@@ -29,6 +29,12 @@ def _get_affine_multifile(files: Sequence[str]):
     Zxyz = np.cross(Xxyz, Yxyz)
     Sx, Sy = ds.ImagePositionPatient[:2]
     Sz = compute_min_slice_loc_multifile(files)
+    # Adjust by table height for Mediso
+    try:
+        if ds.Manufacturer=='Mediso':
+            Sy = Sy - ds.TableHeight
+    except:
+        pass
     M = np.zeros((4, 4))
     M[0] = np.array([dx*Xxyz[0], dy*Yxyz[0], dz*Zxyz[0], Sx])
     M[1] = np.array([dx*Xxyz[1], dy*Yxyz[1], dz*Zxyz[1], Sy])

{pytomography-3.3.0 → pytomography-3.3.2}/src/pytomography/projectors/SPECT/spect_system_matrix.py

@@ -49,8 +49,8 @@ class SPECTSystemMatrix(SystemMatrix):
                     continue
                 img_cutoff = torch.ones(self.object_meta.shape).to(device)
                 img_cutoff[:cutoff_idx, :, :] = 0
-                img_cutoff = pad_object(img_cutoff, mode='replicate')
-                img_cutoff = rotate_detector_z(img_cutoff, -self.proj_meta.angles[i])
+                img_cutoff = pad_object(img_cutoff)
+                img_cutoff = self.rotation_transform.backward(img_cutoff, 270-self.proj_meta.angles[i])
                 img_cutoff = unpad_object(img_cutoff)
                 object_initial *= img_cutoff
         return object_initial

{pytomography-3.3.0 → pytomography-3.3.2}/src/pytomography/utils/simind_mc.py

@@ -204,13 +204,6 @@ def add_together(n_parallel: int, n_windows: int, temp_path: str):
         # REMOVE THESE LATER >
         subprocess.run(['mv', f'temp_output0_tot_w{i+1}.h00', f'tot_w{i+1}.h00'], cwd=temp_path)
         subprocess.run(['sed', '-i', f's/temp_output0_tot_w{i+1}.a00/tot_w{i+1}.a00/g', f'tot_w{i+1}.h00'], cwd=temp_path)
-        # TODO: REMOVE THESE
-        # ---------------
-        # ---------------
-        # ---------------
-        subprocess.run(['cp', f'temp_output0.hct', f'/disk1/er165/lu177_SYME_jaszak_lowres/temp_output0.hct'], cwd=temp_path)
-        subprocess.run(['cp', f'temp_output0.ict', f'/disk1/er165/lu177_SYME_jaszak_lowres/temp_output0.ict'], cwd=temp_path)
-        subprocess.run(['cp', f'temp_output0.res', f'/disk1/er165/lu177_SYME_jaszak_lowres/temp_output0.res'], cwd=temp_path)
                                    
 def run_scatter_simulation(
     source_map: torch.Tensor,
@@ -255,12 +248,16 @@ def run_scatter_simulation(
     # Move simind.smc and energy_resolution.erf to TEMP directory
     module_path = os.path.dirname(os.path.abspath(__file__))
     smc_filepath = os.path.join(module_path, "../data/simind.smc")
-    subprocess.Popen(['cp', smc_filepath, f'{temp_dir.name}/simind.smc']) 
+    p = subprocess.Popen(['cp', smc_filepath, f'{temp_dir.name}/simind.smc']) 
+    p.wait() # wait for copy to complete
     # Create simind commands and run simind in parallel
     simind_commands = [create_simind_command(simind_index_dict, i) for i in range(n_parallel)]
-    procs = [subprocess.Popen([f'simind', 'simind', simind_command, 'radii_corfile.cor'], stdout=subprocess.DEVNULL, cwd=temp_dir.name) for simind_command in simind_commands]
+    procs = [subprocess.Popen([f'simind', 'simind', simind_command, 'radii_corfile.cor'], stdout=subprocess.DEVNULL, stderr=subprocess.PIPE, cwd=temp_dir.name) for simind_command in simind_commands]
     for p in procs:
         p.wait()
+        if p.returncode != 0:  # Check if the process exited with an error
+            error_output = p.stderr.read().decode('utf-8')
+            print(f"Error in process {p.args}:\n{error_output}")
     time.sleep(0.1) # sometimes the last file is not written yet
     # Add together projection data from all seperate processes
     add_together(n_parallel, len(primary_window_idxs), temp_dir.name)
@@ -270,7 +267,7 @@ def run_scatter_simulation(
     temp_dir.cleanup()
     # Return data
     if return_total:
-        return proj_simind_scatter, proj_simind_tot
+        return proj_simind_tot
     else:
         return proj_simind_scatter
 
@@ -309,6 +306,8 @@ class MonteCarloScatterCallback(Callback):
         final_iter: int = np.inf, # when to stop updating scatter
         post_smoothing_sigma_r: float = 0,
         post_smoothing_sigma_z: float = 0,
+        return_total: bool = False,
+        add_to_additive_term: bool = False
     ):
         self.likelihood = likelihood
         self.object_initial = object_initial
@@ -324,6 +323,8 @@ class MonteCarloScatterCallback(Callback):
         self.final_iter = final_iter
         self.post_smoothing_sigma_r = post_smoothing_sigma_r
         self.post_smoothing_sigma_z = post_smoothing_sigma_z
+        self.add_to_additive_term = add_to_additive_term
+        self.return_total = return_total
         self.run_scatter_simulation(object_initial)
         
     def run_scatter_simulation(self, object: torch.Tensor):
@@ -342,6 +343,7 @@ class MonteCarloScatterCallback(Callback):
             simind_index_dict = self.index_dict,
             n_events = self.n_events,   
             n_parallel = self.n_parallel,
+            return_total = self.return_total
         ) / self.calibration_factor * object.sum()
         # Smooth scatter if sigmas are given
         self.scatter_MC = get_smoothed_scatter(
@@ -351,7 +353,10 @@ class MonteCarloScatterCallback(Callback):
             sigma_z = self.post_smoothing_sigma_z
         )
         # Update likelihood
-        self.likelihood.additive_term = self.scatter_MC
+        if self.add_to_additive_term:
+            self.likelihood.additive_term += self.scatter_MC
+        else:
+            self.likelihood.additive_term = self.scatter_MC
         #print(f'Object sum: {object.sum().item()}')
         #print(f'Scatter sum: {self.scatter_MC.sum().item()}')
         #print('-----------------------------------')